The incident happened at the brewer’s Bulmer’s cider plant in August 2014 and was caused when a container of ammonia-contaminated water was emptied into a surface water drain, which is connected to the Widemarsh Brook.
It was estimated that between 2,000 and 3,000 fish were killed, including bullhead, minnows, juvenile chub and dace.
A spokesperson from Heineken confirmed its financial support for two local community organisations, The Wye and Usk Foundation and Bugs and Beasties.
Heineken added: “These important initiatives are making a big difference in our community and to our environment, so we are pleased we can support them.
“Our support has come as part of an agreed settlement with the Environment Agency, relating to an isolated incident that occurred in early 2014. Regrettably, a contractor working on our site failed to dispose of waste material in the correct manner.
“This was a clear breach of our usual policies and industry best practice. Since then, we have cooperated fully with the agency’s investigation and fully accept their findings.”
Significant pollution of one of Hereford's main watercourses
Heineken was among 26 firms that paid out a total of £1.5m to charities as a result of environmental law breaches.
The other businesses ordered to pay fines included Fillippo Foods and Kerry Ingredients.
Heineken had cooperated fully with the Environmental Agency’s investigation and has fully accepted the findings. As a result, the drinks giant has taken steps to tighten its procedures.
Environment Agency spokesperson Dave Throup said: “It’s very unfortunate that a significant pollution of one of Hereford’s main watercourses happened as a result of Heineken’s actions."
Pleased about Heineken's positive contribution
He added: “However, we are pleased that the company is planning to make a positive contribution to the county’s environment by offering this enforcement undertaking.”
Heineken had to pay more than £10,000 after sending 64,600-litres of cider and beer to a nearby effluent treatment plant in 2011.
The brewer has been thrust into the spotlight after it was revealed the brewer is the only remaining bidder for a portfolio of 1,900 Punch pubs.
This came after rival bidder Emerald Investment confirmed that it would not pursue its bid further.